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In this paper, we present a survey of the use of graph theoretical techniques in Biology. In particular, we discuss recent work on identifying and modelling the structure of bio-molecular networks, as well as the application of centrality…
Many cells use calcium signalling to carry information from the extracellular side of the plasma membrane to targets in their interior. Since virtually all cells employ a network of biochemical reactions for Ca2+ signalling, much effort has…
Signal transduction within biological cells is governed by networks of interacting proteins. Communication between these proteins is mediated by signaling molecules which bind to receptors and induce stochastic transitions between different…
The interactions play one of the central roles in the brain mediating various processes and functions. They are particularly important for the brain as a complex system that has many different functions from the same structural…
Ion transport in biological tissues is crucial in the study of many biological and pathological problems. Some multi-cellular structures, like smooth muscles on the vessel walls, could be treated as periodic bi-domain structures, which…
Connected networks are a fundamental structure of neurobiology. Understanding these networks will help us elucidate the neural mechanisms of computation. Mathematically speaking these networks are `graphs' - structures containing objects…
A stochastic model of intracellular calcium oscillations is analytically studied. The governing master equation is expanded under the linear noise approximation and a closed prediction for the power spectrum of fluctuations analytically…
By studying varies dynamical processes, including coupled maps, cellular automata and coupled differential equations, on five different kinds of known networks, we found a positive relation between signal correlation and node's degree. Thus…
The spatial structure of the cell is highly organized at all levels: from small complexes and assemblies, to local nano- and micro-clusters, to global, micrometer scales across and between cells. We suggest that this multiscale spatial cell…
Multicellular organisms comprise a diverse collection of stable tissues built from different cell types. It remains unclear how large numbers of interacting cells can precisely coordinate their gene expression during tissue…
Persistent activity is postulated to drive neural network plasticity and learning. To investigate its underlying cellular mechanisms, we developed a biophysically tractable model that explains the emergence, sustenance, and eventual…
Networked systems display complex patterns of interactions between a large number of components. In physical networks, these interactions often occur along structural connections that link components in a hard-wired connection topology,…
Cells use biochemical networks to translate environmental information into intracellular responses. These responses can be highly dynamic, but how the information is encoded in these dynamics remains poorly understood. Here we investigate…
In this article, we propose a general framework to study the dynamics and topology of cellular networks that capture the geometry of cell packings in two-dimensional tissues. Such epithelia undergo large-scale deformation during…
Exploring the structural topology of genome-based large-scale metabolic network is essential for investigating possible relations between structure and functionality. Visualization would be helpful for obtaining immediate information about…
Coordinated cellular movements are key processes in tissue morphogenesis. Using a cell-based modeling approach we study the dynamics of epithelial layers lining surfaces with constant and varying curvature. We demonstrate that extrinsic…
Many biological, physical, and social interactions have a particular dependence on where they take place. In living cells, protein movement between the nucleus and cytoplasm affects cellular response (i.e., proteins must be present in the…
The organization of cells within tissues plays a vital role in various biological processes, including development and morphogenesis. As a result, understanding how cells self-organize in tissues has been an active area of research. In our…
Most of the calcium in the body is stored in bone. The rest is stored elsewhere, and calcium signalling is one of the most important mechanisms of information propagation in the body. Yet, many questions remain open. In this work, we…
We examine the synchrony of the dynamics of localized [Ca^{2+}]_i oscillations in internal pool of astrocytes via diffusing coupling of a network of such cells in a certain topology where cytosolic Ca^{2+} and inositol 1,4,5-triphosphate…